Added display order number to the severity pyramid rungs, fixed pathogens import for signal sets

Author: dmytrotsko

src/datasources/resources.py

@@ -27,11 +27,21 @@ def process_links(row, dua_column_name="DUA", link_column_name="Link"):
             links.append(link.id)
         else:
             for match in matches:
-                link, _ = Link.objects.get_or_create(url=match[1], defaults={'link_type': match[0], })
+                link, _ = Link.objects.get_or_create(
+                    url=match[1],
+                    defaults={
+                        "link_type": match[0],
+                    },
+                )
                 links.append(link.id)
     row["Links"] = links
 
 
+def process_datasource_name(row):
+    if row["Name"]:
+        row["Name"] = row["Name"].capitalize()
+
+
 def process_datasources(row):
     datasource, _ = DataSource.objects.get_or_create(
         name=row["DB Source"],
@@ -67,5 +77,6 @@ class Meta:
         skip_unchanged = True
 
     def before_import_row(self, row, **kwargs):
+        process_datasource_name(row)
         process_links(row)
         process_datasources(row)

src/fixtures/severity_pyramid_rungs.json

@@ -82,9 +82,10 @@
         "fields": {
             "created": "2024-08-15T09:57:49.327Z",
             "modified": "2024-08-15T13:07:46.136Z",
-            "name": "Population",
-            "display_name": "Population",
-            "used_in": "signal_sets"
+            "name": "Entire Population",
+            "display_name": "Entire Population",
+            "used_in": "signal_sets",
+            "display_order_number": 1
         }
     },
     {
@@ -95,7 +96,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "Vaccinated",
             "display_name": "Vaccinated",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 2
         }
     },
     {
@@ -106,7 +108,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "Infected",
             "display_name": "Infected",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 3
         }
     },
     {
@@ -117,7 +120,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "Tested",
             "display_name": "Tested",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 4
         }
     },
     {
@@ -128,7 +132,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "Ascertained (Case)",
             "display_name": "Ascertained (Case)",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 5
         }
     },
     {
@@ -139,7 +144,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "Symptomatic",
             "display_name": "Symptomatic",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 6
         }
     },
     {
@@ -150,7 +156,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "Outpatient / ED",
             "display_name": "Outpatient / ED",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 7
         }
     },
     {
@@ -161,7 +168,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "Hospitalized",
             "display_name": "Hospitalized",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 8
         }
     },
     {
@@ -172,7 +180,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "ICU",
             "display_name": "ICU",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 9
         }
     },
     {
@@ -183,7 +192,8 @@
             "modified": "2024-08-15T13:07:46.136Z",
             "name": "Deceased",
             "display_name": "Deceased",
-            "used_in": "signal_sets"
+            "used_in": "signal_sets",
+            "display_order_number": 10
         }
     }
 ]

src/signal_sets/forms.py

@@ -35,7 +35,7 @@ class SignalSetFilterForm(forms.ModelForm):
         queryset=SeverityPyramidRung.objects.filter(
             # id__in=SignalSet.objects.values_list("severity_pyramid_rungs", flat="True")
             used_in="signal_sets"
-        ),
+        ).order_by("display_order_number"),
         widget=forms.CheckboxSelectMultiple(),
     )
 

src/signal_sets/resources.py

@@ -221,8 +221,10 @@ def skip_row(self, instance, original, row, import_validation_errors=None):
     def after_import_row(self, row, row_result, **kwargs):
         try:
             signal_set_obj = SignalSet.objects.get(id=row_result.object_id)
+            signal_set_obj.pathogens.clear()
+            signal_set_obj.severity_pyramid_rungs.clear()
+            signal_set_obj.available_geographies.clear()
             for pathogen in row["Pathogen(s)/Syndrome(s)"].split(","):
-                signal_set_obj.pathogens.clear()
                 pathogen = Pathogen.objects.get(name=pathogen, used_in="signal_sets")
                 signal_set_obj.pathogens.add(pathogen)
             for severity_pyramid_rung in row["Surveillance Categories"].split(","):
@@ -231,7 +233,6 @@ def after_import_row(self, row, row_result, **kwargs):
                     used_in="signal_sets"
                 ).first()
                 signal_set_obj.severity_pyramid_rungs.add(severity_pyramid_rung)
-
             for available_geography in row["Geographic Granularity - Delphi"].split(","):
                 available_geography = Geography.objects.get(name=available_geography, used_in="signal_sets")
                 signal_set_obj.available_geographies.add(available_geography)

src/signals/admin.py

@@ -102,6 +102,7 @@ class SeverityPyramidRungAdmin(admin.ModelAdmin):
         "name",
         "display_name",
         "used_in",
+        "display_order_number",
     )
     exclude = ("id",)
     search_fields: tuple[Literal["name"]] = ("name",)

src/signals/migrations/0017_severitypyramidrung_display_order_number.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.0.7 on 2025-03-12 17:52
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('signals', '0016_signal_source_view'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='severitypyramidrung',
+            name='display_order_number',
+            field=models.IntegerField(help_text='Display order number of the severity pyramid rung.', null=True, verbose_name='display order number'),
+        ),
+    ]

src/signals/models.py

@@ -81,6 +81,12 @@ class SeverityPyramidRung(TimeStampedModel):
         default="signals",
     )
 
+    display_order_number: models.IntegerField = models.IntegerField(
+        verbose_name=_("display order number"),
+        help_text=_("Display order number of the severity pyramid rung."),
+        null=True,
+    )
+
     class Meta:
         verbose_name_plural: str = "Severity Pyramid Rungs"
         unique_together: list[str] = ["name", "used_in"]